How To Set The Third Column (Type) Of A Gff File?

Question

[int11ap1]

Hello,

I have a script that computes the number of segregating sites per nucleotide, the Watson estimator (θ), and the nucleotide diversity (π). Once I have these values, I wanna put them into a GFF file. So, I did it. However, the file is not a valid GFF file because the third column (the feature or type) does not have a valid name.

I understand that this column must have a name from the GO reference, but I don't know which name for the three calculations I've done. Do you know something about it?

Thanks in advance.

[ama.biology]

Hello Int11ap1!!

We are looking for a script that computes the number of segregating sites per nucleotide, the Watson estimator (θ), and the nucleotide diversity (π) and we are having many problems to do the script by ourselves. Could you please share your code to inspire us?

Thanks in advance! We would be gratefull for life!!

Answer 1

[Istvan Albert]

Just put a generic term there from the sequence ontology that best describes what you have.

http://www.sequenceontology.org/browser/obob.cgi

[int11ap1]

Ok thanks. Now Gbrowse does not allow me to plot some features as an histogram. There is something special in the GFF file in order to say "hey, I want this feature as an histogram in Gbrowse"?

[Istvan Albert]

Probably but that is GBrowse specific rather than GFF specific, look at the glyphs and other options http://gmod.org/wiki/Glyphs_and_Glyph_Options